d2c7e8be3ceae6027a5274faafdf6239d778cc63
aamp
  Sat Jul 16 08:31:16 2011 -0700
Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
diff --git src/inc/bamUdc.h src/inc/bamUdc.h
deleted file mode 100644
index db82cb8..0000000
--- src/inc/bamUdc.h
+++ /dev/null
@@ -1,132 +0,0 @@
-/* bamFile -- interface to binary alignment format files using Heng Li's samtools lib. */
-
-#ifndef BAMUDC_H
-#define BAMUDC_H
-
-#ifdef USE_BAM
-
-// bam.h is incomplete without _IOLIB set to 1, 2 or 3.  2 is used by Makefile.generic:
-#ifndef _IOLIB
-#define _IOLIB 2
-#endif
-#include "bam.h"
-#include "sam.h"
-
-#else // no USE_BAM
-typedef struct { } bam1_t;
-typedef struct { } samfile_t;
-typedef int (*bam_fetch_f)(const bam1_t *b, void *data);
-
-#define COMPILE_WITH_SAMTOOLS "%s: in order to use this functionality you must " \
-    "install the samtools library (<A HREF=\"http://samtools.sourceforge.net\" " \
-    "TARGET=_BLANK>http://samtools.sourceforge.net</A>) and recompile kent/src with " \
-    "USE_BAM=1 in your environment " \
-    "(see <A HREF=\"http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables\" " \
-    "TARGET=_BLANK>http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables</A>)."
-
-#endif // USE_BAM
-
-#ifndef DNASEQ_H
-#include "dnaseq.h"
-#endif
-
-#ifndef DYSTRING_H
-#include "dystring.h"
-#endif
-
-boolean bamFileExistsUdc(char *bamFileName, char *udcFuseRoot);
-/* Return TRUE if we can successfully open the bam file and its index file. */
-
-samfile_t *bamOpenUdc(char *fileOrUrl, char **retBamFileName, char *udcFuseRoot);
-/* Return an open bam file, dealing with FUSE caching if need be. 
- * Return parameter if NON-null will return the file name after FUSing */
-
-void bamFetchUdc(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
-	samfile_t **pSamFile, char *udcFuseRoot);
-/* Open the .bam file, fetch items in the seq:start-end position range,
- * and call callbackFunc on each bam item retrieved from the file plus callbackData.
- * This handles BAM files with "chr"-less sequence names, e.g. from Ensembl. 
- * The pSamFile parameter is optional.  If non-NULL it will be filled in, just for
- * the benefit of the callback function, with the open samFile.  */
-
-void bamClose(samfile_t **pSamFile);
-/* Close down a samefile_t */
-
-boolean bamIsRc(const bam1_t *bam);
-/* Return TRUE if alignment is on - strand. */
-
-INLINE int bamUnpackCigarElement(unsigned int packed, char *retOp)
-/* Given an unsigned int containing a number of bases and an offset into an
- * array of BAM-enhanced-CIGAR ASCII characters (operations), store operation 
- * char into *retOp (retOp must not be NULL) and return the number of bases. */
-{
-#ifdef USE_BAM
-// decoding lifted from samtools bam.c bam_format1(), long may it remain stable:
-#define BAM_DOT_C_OPCODE_STRING "MIDNSHP"
-int n = packed>>BAM_CIGAR_SHIFT;
-int opcode = packed & BAM_CIGAR_MASK;
-if (opcode >= strlen(BAM_DOT_C_OPCODE_STRING))
-    errAbort("bamUnpackCigarElement: unrecognized opcode %d. "
-	     "(I only recognize 0..%lu [" BAM_DOT_C_OPCODE_STRING "])  "
-	     "Perhaps samtools bam.c's bam_format1 encoding changed?  If so, update me.",
-	     opcode, (unsigned long)(strlen(BAM_DOT_C_OPCODE_STRING)-1));
-*retOp = BAM_DOT_C_OPCODE_STRING[opcode];
-return n;
-#else // no USE_BAM
-errAbort(COMPILE_WITH_SAMTOOLS, "bamUnpackCigarElement");
-return 0;
-#endif// USE_BAM
-}
-
-void bamGetSoftClipping(const bam1_t *bam, int *retLow, int *retHigh, int *retClippedQLen);
-/* If retLow is non-NULL, set it to the number of "soft-clipped" (skipped) bases at
- * the beginning of the query sequence and quality; likewise for retHigh at end.
- * For convenience, retClippedQLen is the original query length minus soft clipping
- * (and the length of the query sequence that will be returned). */
-
-void bamUnpackQuerySequence(const bam1_t *bam, boolean useStrand, char *qSeq);
-/* Fill in qSeq with the nucleotide sequence encoded in bam.  The BAM format 
- * reverse-complements query sequence when the alignment is on the - strand,
- * so if useStrand is given we rev-comp it back to restore the original query 
- * sequence. */
-
-char *bamGetQuerySequence(const bam1_t *bam, boolean useStrand);
-/* Return the nucleotide sequence encoded in bam.  The BAM format 
- * reverse-complements query sequence when the alignment is on the - strand,
- * so if useStrand is given we rev-comp it back to restore the original query 
- * sequence. */
-
-UBYTE *bamGetQueryQuals(const bam1_t *bam, boolean useStrand);
-/* Return the base quality scores encoded in bam as an array of ubytes. */
-
-void bamUnpackCigar(const bam1_t *bam, struct dyString *dyCigar);
-/* Unpack CIGAR string into dynamic string */
-
-char *bamGetCigar(const bam1_t *bam);
-/* Return a BAM-enhanced CIGAR string, decoded from the packed encoding in bam. */
-
-void bamShowCigarEnglish(const bam1_t *bam);
-/* Print out cigar in English e.g. "20 (mis)Match, 1 Deletion, 3 (mis)Match" */
-
-void bamShowFlagsEnglish(const bam1_t *bam);
-/* Print out flags in English, e.g. "Mate is on '-' strand; Properly paired". */
-
-int bamGetTargetLength(const bam1_t *bam);
-/* Tally up the alignment's length on the reference sequence from
- * bam's packed-int CIGAR representation. */
-
-bam1_t *bamClone(const bam1_t *bam);
-/* Return a newly allocated copy of bam. */
-
-void bamShowTags(const bam1_t *bam);
-/* Print out tags in HTML: bold key, no type indicator for brevity. */
-
-char *bamGetTagString(const bam1_t *bam, char *tag, char *buf, size_t bufSize);
-/* If bam's tags include the given 2-character tag, place the value into 
- * buf (zero-terminated, trunc'd if nec) and return a pointer to buf,
- * or NULL if tag is not present. */
-
-void bamUnpackAux(const bam1_t *bam, struct dyString *dy);
-/* Unpack the tag:type:val part of bam into dy */
-
-#endif//ndef BAMUDC_H